Download MendeleyCrystal structure of the SARS-CoV-2 main protease in complex with Z-VAD(OMe)-FMK
Qiao, J.X., Zeng, R., Wang, Y.F., Li, Y.S., Yao, R., Zhou, Y.L., Chen, P., Lei, J., Yang, S.Y.To be published.
7C8B
Crystal structure of the SARS-CoV-2 main protease in complex with Z-VAD(OMe)-FMK
- PDB DOI: 10.2210/pdb7C8B/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2020-05-29 Released: 2020-09-02
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.230
- R-Value Work: 0.177
- R-Value Observed: 0.179
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 3C-like proteinase | A | 306 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt) |  |
UniProt | |||||
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0DTD1 | ||||
Protein Feature ViewExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Z-VAD(OMe)-FMK | B [auth D] | 5 | synthetic construct | Mutation(s): 0 |  |
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CL (Subject of Investigation/LOI) Query on CL | C [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| FL6 Query on FL6 | B [auth D] | L-PEPTIDE LINKING | C5 H9 N O4 |  | ASP |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_002352 Query on PRD_002352 | B [auth D] | Z-VAD(OMe)-FMK | Peptide-like / Inhibitor |  | Ligand Interaction |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.230
- R-Value Work: 0.177
- R-Value Observed: 0.179
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 98.26 | α = 90 |
| b = 82.3 | β = 115.58 |
| c = 51.765 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Deposited Date: 2020-05-29
- Released Date: 2020-09-02 Deposition Author(s): Zeng, R., Qiao, J.X., Wang, Y.F., Li, Y.S., Yao, R., Yang, S.Y., Lei, J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China (NSFC) | China | 2020YFS0010/HX2019nCoV039 |
Revision History (Full details and data files)
- Version 1.0: 2020-09-02
Type: Initial release - Version 1.1: 2021-03-10
Changes: Structure summary
